LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-177-g86abf4f680-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Demonstrate bispectrum computes

# initialize simulation

variable 	nsteps index 0
variable 	nrep equal 2
variable 	a equal 2.0
units		metal

# generate the box and atom positions using a BCC lattice

variable 	nx equal ${nrep}
variable 	nx equal 2
variable 	ny equal ${nrep}
variable 	ny equal 2
variable 	nz equal ${nrep}
variable 	nz equal 2

boundary	p p p

atom_modify	map hash
lattice         bcc $a
lattice         bcc 2
Lattice spacing in x,y,z = 2 2 2
region		box block 0 ${nx} 0 ${ny} 0 ${nz}
region		box block 0 2 0 ${ny} 0 ${nz}
region		box block 0 2 0 2 0 ${nz}
region		box block 0 2 0 2 0 2
create_box	2 box
Created orthogonal box = (0 0 0) to (4 4 4)
  1 by 1 by 1 MPI processor grid
create_atoms	2 box
Created 16 atoms
  using lattice units in orthogonal box = (0 0 0) to (4 4 4)
  create_atoms CPU = 0.001 seconds

mass 		* 180.88

displace_atoms 	all random 0.1 0.1 0.1 123456
Displacing atoms ...

# set up dummy potential to satisfy cutoff
variable 	rcutfac equal 6.0
pair_style 	zero ${rcutfac}
pair_style 	zero 6
pair_coeff 	* *

# set up per-atom computes

compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta 
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 3
inverse polynomial degree: 6
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 0
four-body angular degree: 0
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 0
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 32
number of global descriptors: 32
**************** End of POD Potentials ****************

**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 32
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************

compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta 
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 3
inverse polynomial degree: 6
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 0
four-body angular degree: 0
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 0
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 32
number of global descriptors: 32
**************** End of POD Potentials ****************

**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 32
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************


# set up compute snap generating global array

compute gdd all pod/gdd Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta 
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 3
inverse polynomial degree: 6
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 0
four-body angular degree: 0
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 0
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 32
number of global descriptors: 32
**************** End of POD Potentials ****************

**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 32
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************

#fix 		gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector

compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta 
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 3
inverse polynomial degree: 6
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 0
four-body angular degree: 0
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 0
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 32
number of global descriptors: 32
**************** End of POD Potentials ****************

**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 32
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************

#fix 		ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector

#dump 		mydump_ld all custom 1000 dump_ld id c_ld[*]
#dump 		mydump_dd all custom 1000 dump_dd id c_dd[*]

variable sample_ld1 equal C_ld[1][10]  # Arbitrary local descriptor
fix ldprint all print 1 "${sample_ld1}"

run             ${nsteps}
run             0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87)
WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87)
WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87)
WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8
  ghost atom cutoff = 8
  binsize = 4, bins = 1 1 1
  5 neighbor lists, perpetual/occasional/extra = 1 4 0
  (1) pair zero, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
  (2) compute pod/atom, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (3) compute podd/atom, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (4) compute pod/gdd, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (5) compute pod/ldd, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
0.344594831165384
Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0              0              0              0              0            
Loop time of 1.207e-06 on 1 procs for 0 steps with 16 atoms

165.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 1.207e-06  |            |       |100.00

Nlocal:             16 ave          16 max          16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1984 ave        1984 max        1984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           4311 ave        4311 max        4311 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:         8623 ave        8623 max        8623 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 8623
Ave neighs/atom = 538.9375
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
